Locus 2794

Sequence ID	3L_DroMel_CAF1
Location	7,958,054 – 7,958,160
Length	106
Max. P	0.883013

overview

Window 0

Location	7,958,054 – 7,958,160
Length	106
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	87.57
Mean single sequence MFE	-32.25
Consensus MFE	-23.59
Energy contribution	-26.40
Covariance contribution	2.81
Combinations/Pair	1.03
Mean z-score	-2.27
Structure conservation index	0.73
SVM decision value	0.92
SVM RNA-class probability	0.883013
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958054 106 + 23771897
AGCCUCUUGGCAAGGUGUCUUUGGUCUAGGCUCACUCAGUCACUAACUCACUAGCAACUGAUUCGGCUUAGCCAGU---UCAGUUCCUGUUAUUUUUAGGCUGUGAACC----------
.(((....)))..........(((.(((((((.(.(((((..(((......)))..))))).).))))))))))((---(((...((((.......))))...))))).---------- ( -32.10)
>DroSec_CAF1 3547 109 + 1
AGCCUCUUGGCAAGGUGUCUUUGGUCUAGGCUCACUCAGUCACUAACUCACCAGCAACUGAUUCGGCUUAGCCAGUUGUUCAGUUCCUGUUAUUUUUAGGCUCUGAACC----------
.(((....))).........((((.(((((((.(.(((((..((........))..))))).).)))))))))))..((((((..((((.......))))..)))))).---------- ( -35.10)
>DroSim_CAF1 3548 109 + 1
AGCCUCUUGGCAAGGUGUCUUUGGUCUAGGCUCACUCAGUCACUAACUCACCAGCAACUGAUUCGGCUUAGCCAGUUGUUCAGUUCCUGUUAUUUUUAGGCUCUGAACC----------
.(((....))).........((((.(((((((.(.(((((..((........))..))))).).)))))))))))..((((((..((((.......))))..)))))).---------- ( -35.10)
>DroYak_CAF1 3905 114 + 1
--CCUCUUGGCAAGGUGUCUUUGGUCUAGGCUCACUCAGUCACUAACUCACCAACCACUGAUUCGGCUCGGC---UUAGCCAGUUCCUGUUAUUUUUAGGCUCUGUAGCAGCAACAUCA
--.....((((..((((...(((((...((((.....)))))))))..)))).....((((......)))).---...))))(((.(((((((...........))))))).))).... ( -26.70)
>consensus
AGCCUCUUGGCAAGGUGUCUUUGGUCUAGGCUCACUCAGUCACUAACUCACCAGCAACUGAUUCGGCUUAGCCAGUUGUUCAGUUCCUGUUAUUUUUAGGCUCUGAACC__________
.(((....))).........((((.(((((((.(.(((((..((........))..))))).).)))))))))))..((((((..((((.......))))..))))))........... (-23.59 = -26.40 +   2.81)

alignment

secondary structure

dotplot

Window 1

Location	7,958,054 – 7,958,160
Length	106
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	87.57
Mean single sequence MFE	-31.99
Consensus MFE	-23.46
Energy contribution	-25.15
Covariance contribution	1.69
Combinations/Pair	1.10
Mean z-score	-1.69
Structure conservation index	0.73
SVM decision value	0.30
SVM RNA-class probability	0.672606
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958054 106 - 23771897
----------GGUUCACAGCCUAAAAAUAACAGGAACUGA---ACUGGCUAAGCCGAAUCAGUUGCUAGUGAGUUAGUGACUGAGUGAGCCUAGACCAAAGACACCUUGCCAAGAGGCU
----------(((((((((((...................---...))))........(((((..((((....))))..)))))))))))).................(((....))). ( -31.45)
>DroSec_CAF1 3547 109 - 1
----------GGUUCAGAGCCUAAAAAUAACAGGAACUGAACAACUGGCUAAGCCGAAUCAGUUGCUGGUGAGUUAGUGACUGAGUGAGCCUAGACCAAAGACACCUUGCCAAGAGGCU
----------.((((((..(((.........)))..))))))...((((((.((....(((((..((((....))))..)))))....)).))).)))..........(((....))). ( -34.70)
>DroSim_CAF1 3548 109 - 1
----------GGUUCAGAGCCUAAAAAUAACAGGAACUGAACAACUGGCUAAGCCGAAUCAGUUGCUGGUGAGUUAGUGACUGAGUGAGCCUAGACCAAAGACACCUUGCCAAGAGGCU
----------.((((((..(((.........)))..))))))...((((((.((....(((((..((((....))))..)))))....)).))).)))..........(((....))). ( -34.70)
>DroYak_CAF1 3905 114 - 1
UGAUGUUGCUGCUACAGAGCCUAAAAAUAACAGGAACUGGCUAA---GCCGAGCCGAAUCAGUGGUUGGUGAGUUAGUGACUGAGUGAGCCUAGACCAAAGACACCUUGCCAAGAGG--
.....(..(((((....)))..........(((..(((((((..---(((.(((((......)))))))).)))))))..)))))..).(((......(((....)))......)))-- ( -27.10)
>consensus
__________GGUUCAGAGCCUAAAAAUAACAGGAACUGAACAACUGGCUAAGCCGAAUCAGUUGCUGGUGAGUUAGUGACUGAGUGAGCCUAGACCAAAGACACCUUGCCAAGAGGCU
...........((((((..(((.........)))..))))))...((((((.((....(((((..((((....))))..)))))....)).))).)))......((((.....)))).. (-23.46 = -25.15 +   1.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:49 2006